5jc3 - Revision history

OCA at 10:58, 6 September 2023

OCA — Wed, 06 Sep 2023 10:58:37 GMT

←Older revision		Revision as of 10:58, 6 September 2023
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	==Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (monoclinic form, twinned).==		==Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (monoclinic form, twinned).==
-	<StructureSection load='5jc3' size='340' side='right' caption='[[5jc3]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5jc3' size='340' side='right'caption='[[5jc3]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jc3]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Chick Chick~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jc3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JC3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.6Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MDA5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5jc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc3 OCA], [~~http~~://pdbe.org/5jc3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jc3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jc3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc3 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5jc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc3 OCA], [https://pdbe.org/5jc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jc3 RCSB], [https://www.ebi.ac.uk/pdbsum/5jc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D9N195_CHICK D9N195_CHICK]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chick~~]]	+	[[Category: Gallus gallus]]
-	[[Category: ~~Cusack, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Uchikawa, E~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Dsrna dependent atpase~~]]	+	[[Category: Cusack S]]
-	[[Category: ~~Immune system]]~~	+	[[Category: Uchikawa E]]
-	~~[[Category: Innate immune pattern recognition receptor]]~~	+
-	~~[[Category: Rig-i like helicase]]~~	+
-	~~[[Category: Zinc-containing ctd domain~~]]	+

OCA at 07:12, 21 February 2019

OCA — Thu, 21 Feb 2019 07:12:45 GMT

←Older revision		Revision as of 07:12, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='5jc3' size='340' side='right' caption='[[5jc3]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5jc3' size='340' side='right' caption='[[5jc3]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jc3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jc3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JC3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc3 OCA], [http://pdbe.org/5jc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jc3 RCSB], [http://www.ebi.ac.uk/pdbsum/5jc3 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MDA5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc3 OCA], [http://pdbe.org/5jc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jc3 RCSB], [http://www.ebi.ac.uk/pdbsum/5jc3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jc3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chick]]
	[[Category: Cusack, S]]		[[Category: Cusack, S]]
	[[Category: Uchikawa, E]]		[[Category: Uchikawa, E]]

OCA at 15:34, 1 June 2016

OCA — Wed, 01 Jun 2016 15:34:15 GMT

←Older revision		Revision as of 15:34, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jc3 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (monoclinic form, twinned).==
		+	<StructureSection load='5jc3' size='340' side='right' caption='[[5jc3]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jc3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JC3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jc3 OCA], [http://pdbe.org/5jc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jc3 RCSB], [http://www.ebi.ac.uk/pdbsum/5jc3 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RIG-I and MDA5 sense virus-derived short 5'ppp blunt-ended or long dsRNA, respectively, causing interferon production. Non-signaling LGP2 appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. Co-crystal structures of chicken (ch) LGP2 with dsRNA display a fully or semi-closed conformation depending on the presence or absence of nucleotide. LGP2 caps blunt, 3' or 5' overhang dsRNA ends with 1 bp longer overall footprint than RIG-I. Structures of 1:1 and 2:1 complexes of chMDA5 with short dsRNA reveal head-to-head packing rather than the polar head-to-tail orientation described for long filaments. chLGP2 and chMDA5 make filaments with a similar axial repeat, although less co-operatively for chLGP2. Overall, LGP2 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. Functionally, RNA binding is required for LGP2-mediated enhancement of MDA5 activation. We propose that LGP2 end-binding may promote nucleation of MDA5 oligomerization on dsRNA.

-	~~Authors~~:	+	Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5.,Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S Mol Cell. 2016 May 19;62(4):586-602. doi: 10.1016/j.molcel.2016.04.021. PMID:27203181<ref>PMID:27203181</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jc3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cusack, S]]
		+	[[Category: Uchikawa, E]]
		+	[[Category: Dsrna dependent atpase]]
		+	[[Category: Immune system]]
		+	[[Category: Innate immune pattern recognition receptor]]
		+	[[Category: Rig-i like helicase]]
		+	[[Category: Zinc-containing ctd domain]]

OCA at 15:16, 15 May 2016

OCA — Sun, 15 May 2016 15:16:40 GMT

←Older revision		Revision as of 15:16, 15 May 2016
Line 3:		Line 3:
	The entry 5jc3 is ON HOLD until Paper Publication		The entry 5jc3 is ON HOLD until Paper Publication

-	Authors: ~~Cusack, S., Uchikawa, E.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Cusack, S]]
-	[[Category: Uchikawa, E]]

OCA: Protected "5jc3" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:50:06 GMT

Protected "5jc3" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:50, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jc3 is ON HOLD until Paper Publication Authors: Cusack, S., Uchikawa, E. Description: Category: Unreleased Structures Category: Cusack, S...

OCA — Wed, 11 May 2016 01:50:05 GMT

New page: '''Unreleased structure''' The entry 5jc3 is ON HOLD until Paper Publication Authors: Cusack, S., Uchikawa, E. Description: Category: Unreleased Structures Category: Cusack, S...

New page

'''Unreleased structure'''

The entry 5jc3 is ON HOLD until Paper Publication

Authors: Cusack, S., Uchikawa, E.

Description:
[[Category: Unreleased Structures]]
[[Category: Cusack, S]]
[[Category: Uchikawa, E]]